Put your clif bars away for a sec...A few more options for you guys if you're going there anytime soon. Can any board members vouche for any of these places?
http://search.japantimes.co.jp/cgi-bin/fs20071030a1.html

Wow this is really helpful...
My biggest fear about going there was eating...
now on to fear number 2, language.

There are a few veggie places scattered around Tokyo, Osaka, etc. The problem often is 1) location (finding a place you've never been to can take a good while!) 2) authenticity and pulse. Had a bad experience in Namba (Osaka) hunting an (advertised veggie) place down only to find most options were non-veggie. Places also come and go.

Your best bet is to make due with what's available. A few simple phrases in Japanese can go quite a long way and help you eat at just about any restaurant. However, you do run a small risk that some fish flakes/meat stock or something could appear in a dish. Rule number 1: Stay away from soup and ramen!

In a pinch, you can even find enough to eat at a place like Mos Burger. They can make a veggie rice sandwich thing, and they have salads, etc.

There are also more and more Indian places, as well as a ton of Italianish places if you're really desperate.

I think there are other threads here about eating veggie in Japan. All in all, it's not nearly as difficult to get by as it was 5-10 years ago.